On July 20, 1946, McIntyre was named Coadjutor Archbishop of New York and Titular Archbishop of Paltus. Despite never succeeding Spellman as Archbishop, he greatly assisted in the governance of the Archdiocese while Spellman was busied by his additional duties as Apostolic Vicar for the Military Forces. Spellman once said, "I have never undertaken any important matter without consulting [McIntyre]. In nothing have I gone contrary to his advice."[2] In 1947, he spoke out against legislation that would "permit further encroachments on the parental function of education."[2]

Orthodox in dispositon, McIntyre has been described by Harvard historian Lisa McGirr as "the most extreme right-wing member of the American Catholic hierarchy" during his time.[6] He sent his priests to meetings of the John Birch Society to educate themselves about communism, and recommended subscriptions to American Opinion and other Birch publications in his diocesan newspaper.[6][7] He once expressed caution towards "an obvious trend toward laxity" in the morality of films,[8] and was one of the few American bishops to oppose the liturgical revision of the Second Vatican Council, which he attended from 1962 to 1965.[2][9] On October 23, 1962, McIntyre addressed the Council fathers:

The schema on the Liturgy proposes confusion and complication. If it is adopted, it would be an immediate scandal for our people. The continuity of the Mass must be kept. The tradition of the sacred ceremonies must be preserved....[citation needed],[10]

He also had a noted dispute with the Sisters of the Immaculate Heart of Mary, whom he barred from teaching within the Archdiocese in 1967 after they started promoting liberalism, abandoning their traditional discipline—such as eliminating the habit and compulsory daily prayer.[14] The feud even went to the Vatican, which demanded that the group either restore its former practices or request dispensation from their vows; 315 of the 380 members sought dispensation and formed their own independent organization.[14]

The former tomb of James McIntyre in the crypt of the Cathedral of Our Lady of the Angels, Los Angeles, it has since been moved.

The end of McIntyre's tenure was filled with rancor,[citation needed] as he found himself at odds with blacks, Hispanics, and his own clergy.[dubious– discuss][15] He was once confronted during Mass by the activist Católicos por La Raza, whom he compared to "the rabble at Christ's crucifixion."[citation needed] It is reported[who?] that he harbored racial prejudices and was approached privately by the priests of his archdiocese who asked him to refrain from making racial slurs.[16] He retired after twenty-one years as Archbishop on January 21, 1970, and then served as a parish priest at St. Basil's Church in Downtown Los Angeles, where he privately celebrated the Tridentine Mass on the side altars of St. Basil's.

McIntyre died at St. Vincent Medical Center in Los Angeles, at the age of 93. In 2003, his remains were transferred to the crypt of the new Cathedral of Our Lady of the Angels.

^.Although it has been claimed that the Cardinal made gestures of ecumenism to the Episcopal Church, such a statement was based on the his address to a luncheon of Episcopalian women. See TIME Magazine. Ecumen In March 13, 1964